Additional data 3

Supplementary Table 1: Sheep Chromosome 20 [GenBank: NC_019477.1]Annotated MHC Class 1 region from the NCBI Genome database (November 2014).

Gene Symbol / Gene Name* / Strand / Gene Description / Gene Type / Location
UBD-like / LOC101113965 / + / ubiquitin D-like / protein coding / 28146612..28148999
OR2H1-like / LOC101111325 / - / olfactory receptor 2H1-like / pseudo / c:28130885..28132050
UBD-like / LOC101113705 / - / ubiquitin D-like / protein coding / c: 28111204..28113466
OR2I1-like / LOC101111059 / + / putative olfactory receptor 2I1-like / pseudo / 28106832..28110259
OR2I1-like / LOC101110800 / + / putative olfactory receptor 2I1-like / pseudo / 28097084..28097873
UBD-like / LOC101110547 / - / ubiquitin D-like / protein coding / c: 28090849..28093435
C19orf12-like / LOC101113442 / - / protein C19orf12 homolog / protein coding / c: 28068422..28079358
OR2I1-like / LOC101110278 / + / putative olfactory receptor 2I1-like / pseudo / 28063720..28066582
GABBR1 / + / gamma-aminobutyric acid (GABA) B receptor, 1 / protein coding / 28012311..28056210
MOG / - / myelin oligodendrocyte glycoprotein / protein coding / c: 27997007..28008421
ZFP57 / + / zinc finger protein 57 homolog (mouse) / protein coding / 27992745..27997361
ZNRD1 / - / zinc ribbon domain containing 1 / protein coding / c: 27972373..27975757
PPP1R11 / - / protein phosphatase 1, regulatory (inhibitor) subunit 11 / protein coding / c:27964184..27967320
RNF39 / + / ring finger protein 39 / protein coding / 27934906..27963376
TRNAL-CAA / + / transfer RNA leucine (anticodon CAA) / tRNA / 27931958..27932039
TRIM31 / + / tripartite motif containing 31 / protein coding / 27919516..27930157
TRIM40 / - / tripartite motif containing 40 / protein coding / c:27880429..27891785
TRIM10 / + / tripartite motif containing 10 / protein coding / 27868279..27876934
TRIM15 / - / tripartite motif containing 15 / protein coding / c:27855293..27865217
TRIM26 / + / tripartite motif containing 26 / protein coding / 27829509..27839079
RPF2-like / LOC101111233 / + / ribosome production factor 2 homolog / protein coding / 27814318..27815849
BASP1-like / LOC101110973 / + / brain acid soluble protein 1-like / pseudo / 27803500..27804406
OVAR-MHCI-like / LOC101108963 / - / BOLA class I histocompatibility antigen, alpha chain BL3-6-like / pseudo / c:27766021..27796420
OVAR-MHCI-like / LOC101110710 / - / BOLA class I histocompatibility antigen, alpha chain BL3-7-like / pseudo / c:27673673..27678484
TRIM26-like / LOC101108697 / - / tripartite motif-containing protein 26-like / pseudo / c 27645827..27650044
LOC101108432 / LOC101108432 / + / envelope glycoprotein-like / protein coding / 27604155..27626210
OVAR-MHCI-like / LOC101108171 / - / BOLA class I histocompatibility antigen, alpha chain BL3-7-like / pseudo / c:27596720..27602996
OVAR-MHCI / LOC101107908 / + / BOLA class I histocompatibility antigen, alpha chain BL3-7-like / protein coding / 27566850..27573838
TRIM39-like / LOC101106373 / - / E3 ubiquitin-protein ligase TRIM39-like / protein coding / c:27533628..27542131
ABCF1 / - / ATP-binding cassette, sub-family F (GCN20), member 1 / protein coding / c:27505531..27518579
PRR3 / + / proline rich 3 / protein coding / 27495427..27499481
GNL1 / - / guanine nucleotide binding protein-like 1 / protein coding / c:27486991..27494543
RPP21 / + / ribonuclease P/MRP 21kDa subunit / protein coding / 27460755..27462368
PPP1R10 / + / protein phosphatase 1, regulatory subunit 10 / protein coding / 27446468..27454847
MRPS18B / - / mitochondrial ribosomal protein S18B / protein coding / c:27432758..27439029
ATAT1 / - / alpha tubulin acetyltransferase 1 / protein coding / c:27419172..27431931
C20H6orf136 / - / chromosome 20 open reading frame, human C6orf136 / protein coding / c:27415031..27418766
DHX16 / + / DEAH (Asp-Glu-Ala-His) box polypeptide 16 / protein coding / 27402730..27414855
PPP1R18 / + / protein phosphatase 1, regulatory subunit 18 / protein coding / 27391396..27399789
NRM / + / nurim (nuclear envelope membrane protein) / protein coding / 27386533..27389389
MDC1 / + / mediator of DNA-damage checkpoint 1 / protein coding / 27372265..27383751
TUBB2A / - / tubulin, beta 2A class IIa / protein coding / c:27363398..27367892
FLOT1 / + / flotillin 1 / protein coding / 27352471..27363092
IER3 / + / immediate early response 3 / protein coding / 27350668..27351932
DDR1 / - / discoidin domain receptor tyrosine kinase 1 / protein coding / c: 27239217..27250506
GTF2H4 / - / general transcription factor IIH, polypeptide 4 / protein coding / c: 27223376..27231107
VARS2 / - / valyl-tRNAsynthetase 2, mitochondrial / protein coding / 27210577..27223035
SFTA2 / + / surfactant associated 2 / protein coding / 27206374..27207339
DPCR1-like / LOC101106634 / - / uncharacterized LOC101106634 (DPCR1-like) / protein coding / c: 27187822..27204351
SAP30L-like / LOC101109651 / - / histone deacetylase complex subunit SAP30L-like / pseudo / 27158375..27158905
OVAR-MHCI-like / LOC101106374 / + / BOLA class I histocompatibility antigen, alpha chain BL3-7-like (pseudogene – no transcript) / pseudo / 27133720..27141901
C20H6orf15 / + / chromosome 20 open reading frame, human C6orf15 / protein coding / 27108833..27109953
CDSN / - / corneodesmosin / protein coding / 27100977..27105707
PSORS1C2 / + / psoriasis susceptibility 1 candidate 2 / protein coding / 27083459..27084909
CCHCR1 / + / coiled-coil alpha-helical rod protein 1 / protein coding / 27069757..27081419
TCF19 / - / transcription factor 19 / protein coding / c:27065597..27069326
POU5F1 / + / POU class 5 homeobox 1 / protein coding / 27059785..27064568
MIC-A / LOC101105860 / - / MHC class I polypeptide-related sequence A-like / protein coding / c:27025994..27037088
OVAR-MHCI-like / LOC101107641 / + / BOLA class I histocompatibility antigen, alpha chain BL3-6-like / pseudo / 27016488..27019600
OVAR-MHCI / LOC101105609 / + / BOLA class I histocompatibility antigen, alpha chain BL3-6-like / protein coding / 26967605..26991453
OVAR-MHCI-like / LOC101105367 / + / BOLA class I histocompatibility antigen, alpha chain BL3-7-like / pseudo / 26942864..26967556
IFITM3-like / LOC101110456 / + / interferon-induced transmembrane protein 3-like / pseudo / 26941928..26942348
TSPAN3-like / LOC101105113 / - / tetraspanin-3-like / pseudo / c:26930808..26931445
OVAR-MHCI† / LOC101104866 / + / HLA class I histocompatibility antigen, A-24 alpha chain-like / protein coding / 26924140..26927680
MCCD1 / - / mitochondrial coiled-coil domain 1 / protein coding / c:26897437..26898532
DDX39B / + / spliceosome RNA helicase DDX39B
(BAT1) / protein coding / 26886115..26897170

*Gene Names only provided if different from Gene Symbol. † high similarity to bovine uncharacterised protein MGC126945

Supplementary Table 2: Bovine Chromosome 23 [GenBank: AC_000180.1] Annotated MHC Class 1 region from the NCBI Genome database.

Gene Symbol / Gene Name / Str / Gene Description / Gene Type / Location
OR2I1-like / LOC101903658 / - / putative olfactory receptor 2I1-like / protein coding / c:28921606..28933993
UBD / + / ubiquitin D / 28918428..28920748
OR2H1 / - / olfactory receptor, family 2, subfamily H, member 1 / c:28902250..28918417
OR2H1-like / LOC506486 / - / olfactory receptor, family 2, subfamily H, member 1-like / c:28888958..28892510
UBD-like / LOC504548 / - / ubiquitin D-like / c:28873237..28875584
OR2G3-like / LOC101903577 / + / olfactory receptor 2G3-like / pseudo / 28863423..28871851
C19orf12-like / LOC786987 / - / protein C19orf12 homolog-like / c:28813918..28870287
OR2I1-like / LOC100848480 / + / putative olfactory receptor 2I1-like / pseudo / 28809623..28812480
GABBR1 / gamma-aminobutyric acid (GABA) B receptor, 1 / 28775569..28803896
LOC101906691 / uncharacterized LOC101906691 / ncRNA / 28754175..28759750
MOG / - / myelin oligodendrocyte glycoprotein / c:28738200..28752577
ZFP57 / + / ZFP57 zinc finger protein / 28718554..28739775
ZNRD1 / - / zinc ribbon domain containing 1 / 28714104..28718047
PPP1R11 / - / protein phosphatase 1, regulatory (inhibitor) subunit 11 / c:28707258..28710411
RNF39 / + / ring finger protein 39 / 28701821..28707321
TRNAS-CGA / transfer RNA serine (anticodon CGA) / 28678316..28678397
TRIM31 / tripartite motif containing 31 / 28651502..28677457
TRIM40 / tripartite motif containing 40 / 28625428..28638869, complement
TRIM10 / tripartite motif containing 10 / 28613833..28622421
TRIM15 / tripartite motif containing 15 / 28600324..28611179, complement
TRIM26 / tripartite motif containing 26 / 28562997..28580855
TRIM26-like / LOC526288 / tripartite motif-containing 26 pseudogene / pseudo / 28530732..28543769, complemen
BOLA / MHC class I heavy chain / 28502521..28506312, com
RPL35AP / LOC100295296 / 60S ribosomal protein L35a pseudogene / pseudo / 28494840..28495272, com
BOLA-JSP.1 / MHC Class I JSP.1 / 28469733..28473374, com
LOC100298822 / uncharacterized LOC100298822 / 28425332..28450252, com
BOLA-like / LOC614091 / BOLA class I histocompatibility antigen, alpha chain BL3-7-like / pseudo / 28376891..28431461, com
BOLA-NC1 / non-classical MHC class I antigen / 28351923..28358368, com
BOLA-like / LOC101905956 / BOLA class I histocompatibility antigen, alpha chain BL3-7-like / pseudo / 28330386..28334108, com
BOLA / LOC512672 / major histocompatibility complex, class I / 28299248..28311312
TOM20-like / LOC101906024 / mitochondrial import receptor subunit TOM20 homolog / pseudo / 28297025..28298783, complement
TRIM39 / - / tripartite motif containing 39 (RPP21) / 28257733..28273626, com
GNL1 / + / guanine nucleotide binding protein-like 1 / 28224593..28231252
PRR3 / - / proline rich 3 / 28218614..28223801, com
ABCF1 / - / ATP-binding cassette, sub-family F (GCN20), member 1 / 28198593..28211745, com
PPP1R10 / protein phosphatase 1, regulatory subunit 10 / 28155859..28193657
MRPS18B / mitochondrial ribosomal protein S18B / 28169921..28176935, com
ATAT1 / alpha tubulin acetyltransferase 1 / 28156562..28169425, com
C23H6orf136 / chromosome 23 open reading frame, human C6orf136 / 28152659..28156380, com
DHX16 / DEAH (Asp-Glu-Ala-His) box polypeptide 16 / 28140238..28152495
PPP1R18 / protein phosphatase 1, regulatory subunit 18 / 28128194..28137023
MDC1 / mediator of DNA-damage checkpoint 1 / 28116521..28128504, com
NRM / nurim (nuclear envelope membrane protein) / 28111673..28116241, com
MDC1-like / LOC100336520 / mediator of DNA damage checkpoint protein 1-like / 28107259..28111078
TUBB / tubulin, beta class I / 28100876..28105330, com
FLOT1 / flotillin 1 / 28090029..28100348
IER3 / immediate early response 3 / 28088455..28089726
LOC101905722 / uncharacterized LOC101905722 / ncRNA / 28019005..28036808, com
DDR1 / discoidin domain receptor tyrosine kinase 1 / 27975618..27989666, com
GTF2H4 / general transcription factor IIH, polypeptide 4, 52kDa / 27962143..27968734, com
VARS2 / valyl-tRNAsynthetase 2, mitochondrial (putative) / 27949619..27962028, com
SFTA2 / surfactant associated 2 / 27945517..27946341
DPCR1 / diffuse panbronchiolitis critical region 1 / 27927103..27936148, com
MUC21-like / LOC788774 / mucin-21-like / 27907992..27909549, com
SAP30L-like / LOC787188 / histone deacetylase complex subunit SAP30L-like / 27900050..27900731, com
BOLA-NC1 / non-classical MHC class I antigen / 27862921..27867793
BOLA-like / LOC616942 / major histocompatibility complex, class I, A-like / 27842188..27846500
RRAGC-like / LOC100141101 / ras-related GTP-binding protein C-like / 27835648..27837621, com
C23H6orf15 / chromosome 23 open reading frame, human C6orf15 / 27816299..27817596
CDSN / corneodesmosin / 27808496..27812714
PSORS1C2 / psoriasis susceptibility 1 candidate 2 / 27793273..27794714
CCHCR1 / coiled-coil alpha-helical rod protein 1 / 27779766..27791244
TCF19 / transcription factor 19 / 27775672..27779507, com
POU5F1 / POU class 5 homeobox 1 / 27769893..27774392
MIC1 / major histocompatibility class I related protein / 27659363..27729791 , com
BOLA-like / LOC788634 / BOLA class I histocompatibility antigen, alpha chain BL3-7-like / pseudo / 27715005..27717717
BOLA* / MHC class I heavy chain / 27679384..27692448
BOLA-A / major histocompatibility complex, class I, A / 27646983..27692539
MIC2* / CD99 molecule / 27659409..27666210, com
IFITM3-like / LOC520748 / interferon induced transmembrane protein 3 pseudogene / pseudo / 27646134..27646583
UCR2-like / LOC783502 / cytochrome b-c1 complex subunit 2, mitochondrial pseudogene / pseudo / 27613894..27615466
MGC126945 / uncharacterized protein MGC126945 / 27600073..27604060
MCCD1 / mitochondrial coiled-coil domain 1 / 27576730..27580343, com
DDX39B / DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (Bat1) / 27565924..27576721

*not on current assembly